Divalent ions such as calcium, iron, and copper have roles in physiological functions such as maintaining ionic homeostasis. Ion channels, present in the cell membrane, control the flow of ions across the cell membrane. Hyperkalemic periodic paralysis, iron-deficiency anemia, and horse colic are related to ion channel malfunctions. Equine ion channels have not been studied as much as those in other species. In the present study, we focused on expression and localization of calcium, iron, and copper ion channels in equine duodenum, heart, kidney, liver, lung, ovary, uterus, and testis tissues. Gene and protein expressions were quantified by using real-time polymerase chain reaction and western blotting, respectively. Localization of each channel was identified via immunohistochemical analysis. Gene (mRNA) and protein levels of Nckx3 and Trpv2 were high in uterus tissue. Ferroportin (Ireg1) mRNA levels varied, but its protein level was notably high in liver. Hephaestin (Heph) mRNA level was high in duodenum, whereas its protein level was high in liver. Nckx3 was highly expressed in ovary, uterus, and testis. Trpv2 was expressed in duodenum, liver, lung, and kidney. Ferroportin was expressed in duodenum, liver, ovary, and uterus. Hephaestin was expressed in duodenum, ovary, and testis. Copper transporter 1 (Ctr1) was expressed in all tissues, whereas Atp7a was expressed in duodenum, kidney, and testis. Each protein was expressed in their respective structures, including gland, epithelium, and myocyte. Taken together, the regulation of each ion channel is important to secretion, absorption, and contraction in the various organ. The results of this study could form a basis for elucidating Nckx3-, Trpv2-, Ireg1-, Heph-, Ctr1-, and Atp7a-related diseases in horse.